Fig. 2

Read cloud and short-read genome drafts of Bacteroides caccae obtained from sequencing of stool samples. Circos plots of draft genome assemblies of B. caccae from the sequencing of the patient stool samples are ordered chronologically (A through D) from the outermost inward. Read cloud genome drafts assembled using Athena (blue) are more contiguous and complete than short-read drafts assembled using conventional assembly (gray). The read cloud B. caccae draft from timepoint C (third circos plot from the outside) was the most contiguous and served as the reference for all alignments. Contigs from each read cloud and short-read library are assigned a lighter color if they aligned to this reference, but did not belong to a draft classified as B. caccae. Short reads did not produce a draft annotated as B. caccae for timepoint A. The best read cloud and short-read drafts are both obtained through sequencing of timepoint C (read cloud: 414 kb N50, 5.5 Mb size, 99.3% complete, 1.6% contaminated; short read: 88 kb N50, 4.7 Mb size, 97.7% complete, 0.6% contaminated). The read cloud drafts include a total of 18 assembled integration sites of IS614 (red circles) and 25 assembled integration sites of a candidate insertion sequence (green circles) that are missing from all short-read drafts. Alignments of raw short reads to these sites indicated the presence of both strains without insertion sequence integration and strains with the insertion sequence integration. Estimated proportions of these strains for each site and timepoint are shown with different filled in areas of each circle, with an empty circle denoting predominance of ancestral strains lacking an IS at that location and shaded circles denoting predominance of strains with the IS at that location